Militants burn down Shia houses on August 26, 2012, in the village of Nangkernang in Sampang regency, Madura Island. Hundreds of Sunni militants associated with the Ulema Consensus Forum torched around 50 Shia homes that day, killing one man and seriously injuring another, as several police officers looked on.

© 2012 Saiful Bahri/Antara

The worst fears of the Shia Muslim community in Sampang in Indonesia's East Java came to pass on Aug. 20, 2012. That morning, hundreds of Sunni militants attacked the community, torching some 50 homes, killing one man and seriously injuring another.

The local police, warned ahead of time of the impending violence, stood by at the scene of the attack and refused to intervene. The Sampang regency's top government official dismissed criticism of the police's failure to provide protection for the minority Shia by saying: "I don't care [about] human rights as long I protect those who voted for me as their leader."

The horror endured by the Shia of Sampang stands in stark contrast to the Indonesian government's claims of adherence to the country's constitutional guarantee of religious freedom. A new Human Rights Watch report released Thursday exposes the increasingly routine intimidation, threats, and, too often, violence against Indonesia's religious minorities—and the weak or nonexistent government response.

The minorities in question, including Christian Protestant groups, Shia Muslims, and Ahmadiyahs, typically are targeted by groups such as the Islamic Defenders Front (locally called FPI) that mobilize masses of "protesters" and swarm minority houses of worship. The leaders of such groups say they are defending the Muslim community against "infidels" and "blasphemers." They disrupt the religious observances of minority faiths with loudspeakers and the dumping of animal carcasses and feces on doorsteps.

The tactics of these Islamist militants are growing increasingly violent. According to the Jakarta-based Setara Institute, which monitors religious freedom in Indonesia, religious minorities suffered 264 physical attacks in 2012, up from 216 in 2010.

The most brutal incident targeted an Ahmadiyah group in Cikeusik, Banten province, western Java. On Feb. 6, 2011, some 500 Islamist militants attacked 21 members of the community as they gathered at a private house for prayer, bludgeoning to death three men and seriously injuring five others. A court sentenced 12 of the perpetrators to token prison sentences of three to six months.

Ironically, that same court sentenced an Ahmadiyah man who attempted to defend himself and his community to a six-month prison term. At this writing, almost two years since the attack, the police have not announced the results of their internal investigation into the attack.

The government response to this rising intolerance has been weak at best, and complicit at worst. Officials and security forces frequently facilitate harassment of religious minorities, in some cases even blaming the victims for the attacks. Authorities have made blatantly discriminatory statements, refused to issue building permits for houses of worship, and pressured minority congregations to relocate.

Police often side with Islamist militants at the expense of the rights of minorities, ostensibly to avoid violence. In some cases, police collude with the attackers for religious, economic, or political reasons. In other instances, they lack clear instructions from above or feel outnumbered by militants. In all cases though, the poor police response reflects institutional failure to uphold the law and hold perpetrators of violent crimes to account.

The Religious Affairs Ministry, the Coordinating Board for Monitoring Mystical Beliefs in Society under the Attorney General's Office, and the semi-official Indonesian Ulema Council have all issued decrees and fatwas against members of religious minorities and pressed for the prosecution of "blasphemers." Such behavior contravenes the International Covenant on Civil and Political Rights, which Indonesia ratified in 2005.

So far Indonesian President Susilo Bambang Yudhoyono has been part of the problem. Despite the occasional lofty rhetoric in support of religious tolerance, he has failed to act decisively in support of rule of law and the rights of religious minorities. He has not disciplined members of his government who encourage abuses, including Religious Affairs Minister Suryadharma Ali. At a March 2011 political convention, Mr. Ali exhorted the government "to ban the Ahmadiyah."

Mr. Yudhoyono's weak response has only emboldened hardliners. He can and should revoke laws facilitating religious discrimination, and fully prosecute all those implicated in threats or violence against religious minorities. To prove he's serious, he needs to adopt a "zero tolerance" approach to religious vigilantism. This includes taking disciplinary action against government officials like Mr. Ali.

When U.S. President Barack Obama visited Jakarta in November 2010, he praised "the spirit of religious tolerance that is enshrined in Indonesia's constitution, and that remains one of this country's defining and inspiring characteristics." Almost three years later the deadly indifference of the Yudhoyono government makes a mockery of that statement. Only a vigorous government defense of religious freedom will reverse this course.